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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ), 'gf_id' => 'HOM05D001105', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001105' ), 'data_identifier' => 'HOM05D001105', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001105', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05360' => 'bna', 'A02p05410' => 'bna', 'A03p10590' => 'bna', 'A03p34460' => 'bna', 'A05p42000' => 'bna', 'A08p37440' => 'bna', 'A09p02210' => 'bna', 'A10p01780' => 'bna', 'A10p18670' => 'bna', 'A10p20410' => 'bna', 'Aa31LG11G10420' => 'aar', 'Aa31LG1G9360' => 'aar', 'Aa31LG5G16500' => 'aar', 'Aa31LG5G2430' => 'aar', 'Aa31LG6G11080' => 'aar', 'Aa31sc159G20' => 'aar', 'Aa31sc159G30' => 'aar', 'Actinidia00749' => 'ach', 'Actinidia07280' => 'ach', 'Actinidia08505' => 'ach', 'Actinidia09140' => 'ach', 'Actinidia23497' => 'ach', 'Actinidia35484' => 'ach', 'Actinidia36983' => 'ach', 'Actinidia37059' => 'ach', 'Actinidia40162' => 'ach', 'Ah.15g098960' => 'amhyb', 'AL1G12660' => 'aly', 'AL3G16840' => 'aly', 'AL6G30720' => 'aly', 'AL6G33060' => 'aly', 'AL6G50120' => 'aly', 'Aqoxy1G00642' => 'aox', 'Aqoxy2G03325' => 'aox', 'Aqoxy5G00506' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7RX9RF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KL5RV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P1LIF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0CAB0' => 'arhy', 'AT1G03170' => 'ath', 'AT3G06020' => 'ath', 'AT4G02810' => 'ath', 'AT5G19260' => 'ath', 'AT5G22090' => 'ath', 'ATR0626G041' => 'atr', 'ATR0665G217' => 'atr', 'Atru.chr3.3102' => 'acertr', 'Atru.chr4.2524' => 'acertr', 'Atru.chr5.1433' => 'acertr', 'AUR62020224' => 'cqu', 'AUR62036826' => 'cqu', 'AUR62043169' => 'cqu', 'BcaB01g02000' => 'bca', 'BcaB01g04742' => 'bca', 'BcaB04g19222' => 'bca', 'BcaB05g22751' => 'bca', 'BcaB08g36453' => 'bca', 'BcaB08g36590' => 'bca', 'BcaC01g04318' => 'bca', 'BcaC01g04319' => 'bca', 'BcaC01g06604' => 'bca', 'BcaC03g13658' => 'bca', 'BcaC03g13659' => 'bca', 'BcaC03g13857' => 'bca', 'BcaC04g18586' => 'bca', 'BcaC04g19540' => 'bca', 'BcaC04g24015' => 'bca', 'BcaC04g24016' => 'bca', 'BcaC04g24017' => 'bca', 'BcaC05g24553' => 'bca', 'BcaC05g24632' => 'bca', 'BcaC05g30068' => 'bca', 'BcaNung06067' => 'bca', 'BcaNung06068' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00880' => 'bna', 'BNapus_Darmor_BZH_scaffold_38p02680' => 'bna', 'BolC2t06950H' => 'bol', 'BolC2t07136H' => 'bol', 'BolC3t13692H' => 'bol', 'BolC3t16475H' => 'bol', 'BolC5t28954H' => 'bol', 'BolC5t34784H' => 'bol', 'BolC8t46844H' => 'bol', 'BolC9t53158H' => 'bol', 'BolC9t58327H' => 'bol', 'BolC9t58558H' => 'bol', 'BolC9t58569H' => 'bol', 'BraA02t05494Z' => 'bra', 'BraA02t05637Z' => 'bra', 'BraA03t10371Z' => 'bra', 'BraA03t12623Z' => 'bra', 'BraA05t22921Z' => 'bra', 'BraA08t35642Z' => 'bra', 'BraA09t35870Z' => 'bra', 'BraA10t42453Z' => 'bra', 'BraA10t43947Z' => 'bra', 'BraA10t44111Z' => 'bra', 'C03p12180' => 'bna', 'C03p41920' => 'bna', 'C05p01760' => 'bna', 'C05p61240' => 'bna', 'C08p00450' => 'bna', 'C09p02300' => 'bna', 'C09p54610' => 'bna', 'C09p57020' => 'bna', 'CAN.G1006.12' => 'can', 'CAN.G1463.14' => 'can', 'CAN.G1682.22' => 'can', 'CAN.G226.29' => 'can', 'CAN.G226.30' => 'can', 'CAN.G649.9' => 'can', 'CAN.G689.4' => 'can', 'CAN.G69.20' => 'can', 'CAN.G873.7' => 'can', 'CANSAT25G2825' => 'cansat', 'CANSAT54G2833' => 'cansat', 'CANSAT78G0215' => 'cansat', 'CARHR002510' => 'chi', 'CARHR080520' => 'chi', 'CARHR191440' => 'chi', 'CARHR193700' => 'chi', 'CARHR251180' => 'chi', 'Carub.0001s0231' => 'cru', 'Carub.0003s0544' => 'cru', 'Carub.0006s1759' => 'cru', 'Carub.0006s1973' => 'cru', 'Carub.0006s3425' => 'cru', 'Ca_01631_v3' => 'car', 'Ca_08580_v3' => 'car', 'Ca_10967_v3' => 'car', 'Ca_19474_v3' => 'car', 'Ca_24375_v3' => 'car', 'Cc01_g07830' => 'ccan', 'Cc01_g19510' => 'ccan', 'Cc03_g03370' => 'ccan', 'CDE02G1564' => 'cde', 'CDE05G0165' => 'cde', 'CDE05G1291' => 'cde', 'CDE06G0576' => 'cde', 'CDE06G2280' => 'cde', 'CDE08G0758' => 'cde', 'CDE11G0126' => 'cde', 'Cfa006135' => 'cfa', 'Cfa010179' => 'cfa', 'Cfa015607' => 'cfa', 'Ciclev10005417m.g' => 'ccl', 'Ciclev10021186m.g' => 'ccl', 'Ciclev10028116m.g' => 'ccl', 'CiPaw.01G162700' => 'cil', 'CiPaw.02G094400' => 'cil', 'CiPaw.07G091300' => 'cil', 'CiPaw.08G105300' => 'cil', 'CiPaw.13G128900' => 'cil', 'CiPaw.14G094000' => 'cil', 'ClCG02G022450' => 'cla', 'ClCG03G012250' => 'cla', 'ClCG06G005960' => 'cla', 'ClCG09G007020' => 'cla', 'COL.COLO4_05832' => 'col', 'COL.COLO4_09100' => 'col', 'COL.COLO4_20684' => 'col', 'COL.COLO4_20687' => 'col', 'COL.COLO4_20688' => 'col', 'COL.COLO4_20689' => 'col', 'COL.COLO4_25412' => 'col', 'COL.COLO4_35348' => 'col', 'Cpa.g.c33086' => 'cpa', 'CsaV3_1G043850' => 'csa', 'CsaV3_3G013540' => 'csa', 'CsaV3_6G037110' => 'csa', 'CsaV3_6G038310' => 'csa', 'CsaV3_6G038580' => 'csa', 'CsaV3_7G028140' => 'csa', 'CSS0018072' => 'camsi', 'CSS0019741' => 'camsi', 'CSS0023684' => 'camsi', 'CSS0029817' => 'camsi', 'CSS0044577' => 'camsi', 'CSS0049503' => 'camsi', 'DCAR_002399' => 'dca', 'DCAR_002708' => 'dca', 'DCAR_012473' => 'dca', 'DCAR_012502' => 'dca', 'DCAR_018418' => 'dca', 'DCAR_027170' => 'dca', 'DCAR_030614' => 'dca', 'Dinv18846' => 'din', 'Dinv32938' => 'din', 'Dinv33540' => 'din', 'Dinv38413' => 'din', 'Dinv44502' => 'din', 'Duzib133G0922' => 'dzi', 'Duzib133G0996' => 'dzi', 'Duzib138G1156' => 'dzi', 'Duzib150G1443' => 'dzi', 'Duzib151G0714' => 'dzi', 'Duzib168G1448' => 'dzi', 'Duzib170G0012' => 'dzi', 'Duzib211G0127' => 'dzi', 'Duzib212G0111' => 'dzi', 'ECA236G2824' => 'eca', 'ECA238G3180' => 'eca', 'ECA240G3199' => 'eca', 'EL10Ac7g16289' => 'bvu', 'EL10Ac7g17229' => 'bvu', 'EL10As3g23327' => 'bvu', 'Eucgr.B01102' => 'egr', 'Eucgr.H01483' => 'egr', 'Eucgr.H01485' => 'egr', 'Eucgr.H03564' => 'egr', 'Eucgr.J00324' => 'egr', 'Eucgr.J00576' => 'egr', 'FAN07G1906' => 'fan', 'FAN11G1461' => 'fan', 'FAN12G2450' => 'fan', 'FAN15G2811' => 'fan', 'FAN16G3495' => 'fan', 'FAN17G2206' => 'fan', 'FAN20G3052' => 'fan', 'FAN21G1882' => 'fan', 'FAN22G2240' => 'fan', 'FAN24G3176' => 'fan', 'FAN25G0372' => 'fan', 'FAN27G2256' => 'fan', 'FAN27G3210' => 'fan', 'FvH4_2g23620' => 'fve', 'FvH4_3g26310' => 'fve', 'FvH4_4g14940' => 'fve', 'Glyma.01G239800' => 'gma', 'Glyma.02G147500' => 'gma', 'Glyma.03G153400' => 'gma', 'Glyma.10G026300' => 'gma', 'Glyma.10G250700' => 'gma', 'Glyma.11G003900' => 'gma', 'Glyma.11G177001' => 'gma', 'Glyma.12G095200' => 'gma', 'Glyma.12G189300' => 'gma', 'Glyma.13G312500' => 'gma', 'Glyma.19G155800' => 'gma', 'Glyma.20G143000' => 'gma', 'Gohir.A05G077900' => 'ghi', 'Gohir.A07G113500' => 'ghi', 'Gohir.A08G067600' => 'ghi', 'Gohir.A09G100100' => 'ghi', 'Gohir.A09G213800' => 'ghi', 'Gohir.A11G122500' => 'ghi', 'Gohir.A12G005200' => 'ghi', 'Gohir.D05G080700' => 'ghi', 'Gohir.D07G117200' => 'ghi', 'Gohir.D08G076000' => 'ghi', 'Gohir.D09G099500' => 'ghi', 'Gohir.D09G216300' => 'ghi', 'Gohir.D11G127800' => 'ghi', 'Gohir.D12G004700' => 'ghi', 'Gorai.001G126000' => 'gra', 'Gorai.004G080300' => 'gra', 'Gorai.006G116500' => 'gra', 'Gorai.006G236700' => 'gra', 'Gorai.007G136700' => 'gra', 'Gorai.008G004600' => 'gra', 'Gorai.009G082500' => 'gra', 'GSVIVG01011086001' => 'vvi', 'GSVIVG01017917001' => 'vvi', 'GSVIVG01024498001' => 'vvi', 'GSVIVG01037588001' => 'vvi', 'HanXRQChr01g0003151' => 'han', 'HanXRQChr04g0118271' => 'han', 'HanXRQChr09g0250261' => 'han', 'HanXRQChr10g0291611' => 'han', 'HanXRQChr14g0431681' => 'han', 'Haze_00938' => 'cav', 'Haze_04713' => 'cav', 'Haze_23569' => 'cav', 'Hma1.2p1_0101F.1_g049530' => 'hma', 'Hma1.2p1_0434F.1_g152200' => 'hma', 'Hma1.2p1_0995F.1_g245700' => 'hma', 'HPP92_002189' => 'vpl', 'HPP92_004124' => 'vpl', 'HPP92_013316' => 'vpl', 'HPP92_013317' => 'vpl', 'HPP92_019218' => 'vpl', 'HPP92_025059' => 'vpl', 'Hund12169' => 'sun', 'Hund20949' => 'sun', 'Lalb_Chr01g0005041' => 'lal', 'Lalb_Chr02g0142791' => 'lal', 'Lalb_Chr03g0028441' => 'lal', 'Lalb_Chr06g0163011' => 'lal', 'Lalb_Chr06g0164801' => 'lal', 'Lalb_Chr09g0319701' => 'lal', 'Lalb_Chr16g0376381' => 'lal', 'Lalb_Chr19g0136231' => 'lal', 'Lalb_Chr21g0306481' => 'lal', 'Lalb_Chr21g0307801' => 'lal', 'Lalb_Chr24g0393361' => 'lal', 'Lj1g0015154' => 'lja', 'Lj1g0027615' => 'lja', 'Lj2P1173T12' => 'lonja', 'Lj2P957T12' => 'lonja', 'Lj3g0000688' => 'lja', 'Lj3g0020217' => 'lja', 'Lj3P741T21' => 'lonja', 'Lj5g0001986' => 'lja', 'Lj5g0002837' => 'lja', 'Lsat_1_v5_gn_2_35160' => 'lsa', 'Lsat_1_v5_gn_5_188280' => 'lsa', 'Lsat_1_v5_gn_5_74260' => 'lsa', 'Lsat_1_v5_gn_6_115140' => 'lsa', 'Lsat_1_v5_gn_7_66720' => 'lsa', 'Lsat_1_v5_gn_8_56341' => 'lsa', 'Manes.01G207900' => 'mes', 'Manes.03G181900' => 'mes', 'Manes.04G062200' => 'mes', 'Manes.05G076000' => 'mes', 'Manes.15G025700' => 'mes', 'MBI03_g11328_MAGBIO' => 'mbi', 'MBI06_g01086_MAGBIO' => 'mbi', 'MBI06_g47796_MAGBIO' => 'mbi', 'MBI17_g45764_MAGBIO' => 'mbi', 'MBI19_g16317_MAGBIO' => 'mbi', 'MD03G1156200' => 'mdo', 'MD03G1265600' => 'mdo', 'MD11G1173900' => 'mdo', 'MD11G1286200' => 'mdo', 'MD13G1186600' => 'mdo', 'MD16G1187300' => 'mdo', 'Medtr1g105075' => 'mtr', 'Medtr1g105360' => 'mtr', 'Medtr2g087390' => 'mtr', 'Medtr2g087430' => 'mtr', 'Medtr2g087460' => 'mtr', 'Medtr2g087470' => 'mtr', 'Medtr4g050590' => 'mtr', 'Medtr5g005770' => 'mtr', 'Medtr7g094830' => 'mtr', 'MELO3C006550.2' => 'cme', 'MELO3C014402.2' => 'cme', 'MELO3C014495.2' => 'cme', 'MELO3C014521.2' => 'cme', 'MELO3C015055.2' => 'cme', 'MELO3C015838.2' => 'cme', 'Migut.D02383' => 'egut', 'Migut.G00312' => 'egut', 'Migut.O00517' => 'egut', 'Migut.O00651' => 'egut', 'Migut.O00962' => 'egut', 'MSTRG.10002' => 'ama', 'MSTRG.12397' => 'ama', 'MSTRG.18796' => 'ama', 'MSTRG.21008' => 'ama', 'MSTRG.24751' => 'ama', 'Nitab4.5_0000157g0160' => 'nta', 'Nitab4.5_0000295g0230' => 'nta', 'Nitab4.5_0000321g0040' => 'nta', 'Nitab4.5_0000458g0040' => 'nta', 'Nitab4.5_0000630g0170' => 'nta', 'Nitab4.5_0000759g0130' => 'nta', 'Nitab4.5_0000875g0110' => 'nta', 'Nitab4.5_0001504g0090' => 'nta', 'Nitab4.5_0002792g0060' => 'nta', 'Nitab4.5_0003538g0010' => 'nta', 'Nitab4.5_0003657g0020' => 'nta', 'Nitab4.5_0006145g0010' => 'nta', 'Nitab4.5_0006390g0040' => 'nta', 'Nitab4.5_0008364g0020' => 'nta', 'Nitab4.5_0008797g0040' => 'nta', 'Nn2g14335' => 'nnu', 'Nn6g34663' => 'nnu', 'Oeu004491.1' => 'oeu', 'Oeu015971.1' => 'oeu', 'Oeu022873.1' => 'oeu', 'Oeu026358.1' => 'oeu', 'Oeu029584.1' => 'oeu', 'Oeu030328.1' => 'oeu', 'Oeu044522.1' => 'oeu', 'Oeu048824.1' => 'oeu', 'Oeu051475.1' => 'oeu', 'Oeu058193.2' => 'oeu', 'Os01g0302250' => 'osa', 'Os03g0261800' => 'osa', 'Os03g0705800' => 'osa', 'Peaxi162Scf00098g00112' => 'pax', 'Peaxi162Scf00161g00111' => 'pax', 'Peaxi162Scf00345g00065' => 'pax', 'Peaxi162Scf00429g00042' => 'pax', 'Peaxi162Scf00769g00043' => 'pax', 'Peaxi162Scf00783g00032' => 'pax', 'Peaxi162Scf01336g00015' => 'pax', 'Peaxi162Scf01607g00012' => 'pax', 'PGR004G0344' => 'pgr', 'PGR044G1104' => 'pgr', 'PGR119G1719' => 'pgr', 'PGR119G2523' => 'pgr', 'PGR142G1445' => 'pgr', 'PGR142G4453' => 'pgr', 'PGSC0003DMG400002999' => 'stu', 'PGSC0003DMG400005904' => 'stu', 'PGSC0003DMG400009028' => 'stu', 'PGSC0003DMG400011821' => 'stu', 'PGSC0003DMG400012882' => 'stu', 'PGSC0003DMG400013130' => 'stu', 'PGSC0003DMG400013134' => 'stu', 'PGSC0003DMG400014641' => 'stu', 'PGSC0003DMG400020124' => 'stu', 'Phvul.001G150800' => 'pvu', 'Phvul.002G047700' => 'pvu', 'Phvul.005G118900' => 'pvu', 'Phvul.007G053800' => 'pvu', 'Phvul.007G171900' => 'pvu', 'Phvul.011G099500' => 'pvu', 'Potri.001G216000' => 'ptr', 'Potri.002G053400' => 'ptr', 'Potri.005G209100' => 'ptr', 'Potri.008G149600' => 'ptr', 'Potri.009G016600' => 'ptr', 'Potri.010G091800' => 'ptr', 'Prupe.1G154300' => 'ppe', 'Prupe.6G145500' => 'ppe', 'Prupe.8G241400' => 'ppe', 'Psat3g065280' => 'psa', 'Psat4g211120' => 'psa', 'Psat5g260920' => 'psa', 'Psat5g261120' => 'psa', 'Psat6g209440' => 'psa', 'Psat6g209920' => 'psa', 'Psat7g204640' => 'psa', 'PSO170G3767' => 'pso', 'PSO210G4597' => 'pso', 'PSO302G0035' => 'pso', 'PSO675G0144' => 'pso', 'PSO675G4832' => 'pso', 'PSO675G6621' => 'pso', 'PSO675G7239' => 'pso', 'PSO675G7257' => 'pso', 'PSO717G0007' => 'pso', 'PSO717G0033' => 'pso', 'PSO717G0050' => 'pso', 'PSO717G0114' => 'pso', 'PSO717G0121' => 'pso', 'PSO717G0131' => 'pso', 'PSO832G4048' => 'pso', 'QL01p019511' => 'qlo', 'QL06p003612' => 'qlo', 'QL10p014790' => 'qlo', 'QL12p021926' => 'qlo', 'QL12p022331' => 'qlo', 'RcHm_v2.0_Chr4g0417161' => 'rch', 'RcHm_v2.0_Chr5g0048601' => 'rch', 'RcHm_v2.0_Chr6g0291081' => 'rch', 'Rhsim01G0200900' => 'rsi', 'Rhsim02G0022200' => 'rsi', 'Rhsim04G0204100' => 'rsi', 'Rhsim13G0024500' => 'rsi', 'Sabra02G0043500' => 'sbr', 'Sabra05G0159200' => 'sbr', 'Sabra08G0113700' => 'sbr', 'Sabra10G0051500' => 'sbr', 'Sabra16G0127700' => 'sbr', 'SalBow2G0923' => 'sbo', 'SalBow4G2473' => 'sbo', 'SalBow6G1282' => 'sbo', 'SalBow6G3058' => 'sbo', 'Sc05g0004950' => 'sci', 'Sc13g0004160' => 'sci', 'Sc21g0006780' => 'sci', 'Sed0008439' => 'sed', 'Sed0010927' => 'sed', 'Sed0014733' => 'sed', 'Sed0016607' => 'sed', 'Sed0020706' => 'sed', 'Sed0024938' => 'sed', 'Sed0025701' => 'sed', 'SEGI_06592' => 'sgi', 'SGA_v2.0_scaffold11G05808' => 'sas', 'SGA_v2.0_scaffold1G00470' => 'sas', 'SGA_v2.0_scaffold22G09821' => 'sas', 'SGA_v2.0_scaffold237G43801' => 'sas', 'SGA_v2.0_scaffold39G15299' => 'sas', 'SGA_v2.0_scaffold80G25936' => 'sas', 'SHI14597' => 'shi', 'Solyc01g009260.1' => 'sly', 'Solyc01g009270.1' => 'sly', 'Solyc06g008990.1' => 'sly', 'Solyc06g054310.1' => 'sly', 'Solyc06g084280.1' => 'sly', 'Solyc09g065140.1' => 'sly', 'Solyc11g071940.1' => 'sly', 'Sopen01g004750' => 'spe', 'Sopen01g004760' => 'spe', 'Sopen01g031500' => 'spe', 'Sopen06g003770' => 'spe', 'Sopen06g019420' => 'spe', 'Sopen06g030340' => 'spe', 'Sopen06g035670' => 'spe', 'Sopen11g029610' => 'spe', 'Sp1g02190' => 'spa', 'Sp3g04960' => 'spa', 'Sp6g02840' => 'spa', 'Sp6g23100' => 'spa', 'Sp6g25150' => 'spa', 'TAR362G0629' => 'tar', 'TAR365G0527' => 'tar', 'TAR623G1713' => 'tar', 'TAR633G0419' => 'tar', 'TAR636G1608' => 'tar', 'TAR636G2506' => 'tar', 'THA.LOC104799569' => 'tha', 'THA.LOC104800506' => 'tha', 'THA.LOC104801234' => 'tha', 'THA.LOC104810935' => 'tha', 'THA.LOC104816974' => 'tha', 'THA.LOC104818809' => 'tha', 'THA.LOC104823091' => 'tha', 'THA.LOC104823093' => 'tha', 'Thecc.01G279800' => 'tca', 'Thecc.04G226200' => 'tca', 'Thecc.09G271400' => 'tca', 'Thhalv10008552m.g' => 'esa', 'Thhalv10013382m.g' => 'esa', 'Thhalv10015905m.g' => 'esa', 'Thhalv10022430m.g' => 'esa', 'Thhalv10029267m.g' => 'esa', 'TPR.G38020' => 'tpr', 'TPR.G4175' => 'tpr', 'TPR.G4653' => 'tpr', 'TPR.G5460' => 'tpr', 'TPR.G9929' => 'tpr', 'TWI09G1192' => 'twi', 'TWI14G0758' => 'twi', 'TWI23G0440' => 'twi', 'TWI31G0854' => 'twi', 'TWI59G0570' => 'twi', 'TWI73G1145' => 'twi', 'TWI79G1166' => 'twi', 'unitig_22.g5258' => 'ugi', 'unitig_26.g10152' => 'ugi', 'unitig_26.g9418' => 'ugi', 'unitig_26.g9419' => 'ugi', 'unitig_32.g10808' => 'ugi', 'unitig_749.g13604' => 'ugi', 'unitig_749.g14069' => 'ugi', 'vmacro02568' => 'vma', 'VMungo0720G0888' => 'vmu', 'VMungo0720G2733' => 'vmu', 'VMungo1080G1577' => 'vmu', 'VMungo1127G0292' => 'vmu', 'VMungo1127G0986' => 'vmu', 'VMungo1215G0742' => 'vmu', 'VMungo1383G0841' => 'vmu', 'Zm00001eb011430' => 'zma', 'Zm00001eb054430' => 'zma', 'Zm00001eb216640' => 'zma', 'Zm00001eb398180' => 'zma' ) $gf_id = 'HOM05D001105' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001105' ) $data_identifier = 'HOM05D001105' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 7, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 11, 'bra' => (int) 10, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 8, 'cpa' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 11, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 6, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 2, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 6, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 8, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 1, 'vmu' => (int) 7, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398180' $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